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- PDB-5uy3: Crystal structure of human Fab PGT144, a broadly reactive and pot... -

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Basic information

Entry
Database: PDB / ID: 5uy3
TitleCrystal structure of human Fab PGT144, a broadly reactive and potent HIV-1 neutralizing antibody
Components
  • Antibody PGT144 Fab heavy chain
  • Antibody PGT144 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / HIV Env glycoprotein
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJulien, J.-P. / Lee, J.H. / Wilson, I.A.
Funding support United States, 5items
OrganizationGrant numberCountry
California HIV/AIDS Research Program Dissertation AwardD12-SRI-353 United States
Scripps CHAVI-IDUM1 AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110657 United States
International AIDS Vaccine Initiative United States
Bill & Melinda Gates FoundationOPP1115782 and OPP1084519 United States
CitationJournal: Immunity / Year: 2017
Title: A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic β-Hairpin Structure.
Authors: Jeong Hyun Lee / Raiees Andrabi / Ching-Yao Su / Anila Yasmeen / Jean-Philippe Julien / Leopold Kong / Nicholas C Wu / Ryan McBride / Devin Sok / Matthias Pauthner / Christopher A Cottrell / ...Authors: Jeong Hyun Lee / Raiees Andrabi / Ching-Yao Su / Anila Yasmeen / Jean-Philippe Julien / Leopold Kong / Nicholas C Wu / Ryan McBride / Devin Sok / Matthias Pauthner / Christopher A Cottrell / Travis Nieusma / Claudia Blattner / James C Paulson / Per Johan Klasse / Ian A Wilson / Dennis R Burton / Andrew B Ward /
Abstract: Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the ...Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the surface HIV envelope (Env) trimer. Using cryo-electron microscopy, we solved the atomic structure of an apex bnAb, PGT145, in complex with Env. We showed that the long anionic HCDR3 of PGT145 penetrated between glycans at the trimer 3-fold axis, to contact peptide residues from all three Env protomers, and thus explains its highly trimer-specific nature. Somatic hypermutation in the other CDRs of PGT145 were crucially involved in stabilizing the structure of the HCDR3, similar to bovine antibodies, to aid in recognition of a cluster of conserved basic residues hypothesized to facilitate trimer disassembly during viral entry. Overall, the findings exemplify the creative solutions that the human immune system can evolve to recognize a conserved motif buried under a canopy of glycans.
History
DepositionFeb 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Antibody PGT144 Fab light chain
H: Antibody PGT144 Fab heavy chain
B: Antibody PGT144 Fab light chain
A: Antibody PGT144 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)98,8704
Polymers98,8704
Non-polymers00
Water0
1
L: Antibody PGT144 Fab light chain
H: Antibody PGT144 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)49,4352
Polymers49,4352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-23 kcal/mol
Surface area20460 Å2
MethodPISA
2
B: Antibody PGT144 Fab light chain
A: Antibody PGT144 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)49,4352
Polymers49,4352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-23 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.600, 67.550, 69.550
Angle α, β, γ (deg.)82.04, 74.89, 81.26
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Antibody PGT144 Fab light chain


Mass: 23560.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody PGT144 Fab heavy chain


Mass: 25874.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: JCSG F8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 21292 / % possible obs: 96.6 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U1S
Resolution: 2.9→36.293 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 2.08 / Phase error: 30.9
RfactorNum. reflection% reflection
Rfree0.2821 1064 5 %
Rwork0.2409 --
obs0.243 21284 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→36.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 0 0 6856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037021
X-RAY DIFFRACTIONf_angle_d0.6199541
X-RAY DIFFRACTIONf_dihedral_angle_d16.2444171
X-RAY DIFFRACTIONf_chiral_restr0.0431062
X-RAY DIFFRACTIONf_plane_restr0.0041215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.0320.41311330.32032541X-RAY DIFFRACTION97
3.032-3.19170.32891330.29342530X-RAY DIFFRACTION97
3.1917-3.39150.30881350.26482566X-RAY DIFFRACTION97
3.3915-3.65320.30661320.25652508X-RAY DIFFRACTION97
3.6532-4.02040.28211320.2422508X-RAY DIFFRACTION96
4.0204-4.60120.26481330.21432529X-RAY DIFFRACTION96
4.6012-5.79320.20711340.22524X-RAY DIFFRACTION97
5.7932-36.29590.26811320.22232514X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.02180.01160.00390.022-0.01050.00140.0110.0398-0.1344-0.04250.05480.0041-0.00070.074900.37590.0353-0.04160.5146-0.0630.250810.3934-6.718326.9997
20.0099-0.0220.02830.0009-0.03110.01880.1708-0.1909-0.1348-0.15470.03730.1924-0.09320.131500.23530.0251-0.01670.3304-0.23960.061910.27521.427426.3122
30.0059-0.01440.0044-0.0165-0.02620.04920.10630.1062-0.0346-0.03240.0076-0.051-0.0645-0.113400.2427-0.0062-0.0010.2079-0.00690.2619-2.29877.972858.5671
40.03440.0133-00.03150.0064-0.01650.04890.01160.00910.0863-0.07750.0503-0.02940.0778-00.1805-0.0130.0050.12550.00290.2043-2.86898.129261.1826
5-0.002-0.00520.0071-0.0043-0.01370.0111-0.0782-0.01510.0776-0.05080.08370.0428-0.1154-0.0787-00.52680.08720.09160.5688-0.11160.4016-9.867914.508220.3876
6-0.07890.0166-0.0035-0.001-0.0050.0152-0.17030.21110.1588-0.2471-0.3802-0.21420.17520.16920-0.70940.2275-0.3363-0.8353-0.8949-0.8441-6.08572.41114.861
70.0001-0.02170.0388-0.01430.025-0.00440.00250.0991-0.23390.0746-0.3028-0.025-0.2617-0.046-00.15770.11320.0119-0.3921-0.03580.1369-6.648621.655151.1424
80.0191-0.02380.0250.02280.01780.03460.08720.1017-0.12570.01660.14960.02930.05880.002300.3065-0.08670.0640.3546-0.02020.20217.205433.60523.5332
90.03310.0160.01810.0121-0.0117-0.00330.20880.1206-0.2141-0.0595-0.032-0.2328-0.1295-0.14250-0.4384-0.32230.06940.30360.10890.2577.873433.588817.8268
100.0002-0.0047-0.00090.02890.01210.02770.11740.03430.15860.1914-0.04110.15030.07150.148800.1417-0.0274-0.01430.13840.04520.187925.066139.3036-10.5953
110.0450.03290.01990.0452-0.02040.00220.0276-0.0551-0.0357-0.0855-0.0082-0.01490.0372-0.040700.33710.01850.04550.17870.04520.235423.538236.112-12.0249
120.00280.00790.00030.00270.00010.0021-0.00540.023-0.0383-0.00970.0176-0.00350.00610.067700.2288-0.08730.22350.4877-0.03130.375237.372238.391522.2988
130.0040.00510.00480.0031-0.00180.0029-0.02180.05890.0381-0.0355-0.0134-0.0742-0.02370.022600.4006-0.00470.07690.234-0.00870.188527.380546.076537.5154
140.00580.0153-0.0031-0.01020.0062-0.00110.00360.0570.0134-0.03630.04860.04090.08930.0125-00.15160.1037-0.04090.3440.05310.181824.490133.170525.6176
15-0.0010.0021-0.00470.0039-0.00880.00350.07440.0336-0.1473-0.00280.0330.01020.00510.039200.4664-0.0793-0.01610.0950.15650.119826.785329.290335.6052
16-0.01990.05320.0177-0.0024-0.00390.01920.08610.1578-0.12990.1440.18160.03740.2097-0.107600.08920.1417-0.15340.06380.1479-0.006328.155732.8832.9478
170.01180.00560.01220.00730.00580.0091-0.00330.12820.12890.0393-0.20150.10220.0515-0.008700.3915-0.0687-0.02690.29680.05250.187119.601430.839540.5476
18-0.0149-0.05830.0458-0.0396-0.00420.01440.0392-0.0660.01650.06270.01130.0661-0.08360.053900.1083-0.01920.02030.14030.01130.175430.530549.1955-1.7449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 2 through 32 )
2X-RAY DIFFRACTION2chain 'L' and (resid 33 through 102 )
3X-RAY DIFFRACTION3chain 'L' and (resid 103 through 160 )
4X-RAY DIFFRACTION4chain 'L' and (resid 161 through 212 )
5X-RAY DIFFRACTION5chain 'H' and (resid 4 through 32 )
6X-RAY DIFFRACTION6chain 'H' and (resid 33 through 116 )
7X-RAY DIFFRACTION7chain 'H' and (resid 117 through 218 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 61 )
9X-RAY DIFFRACTION9chain 'B' and (resid 62 through 113 )
10X-RAY DIFFRACTION10chain 'B' and (resid 114 through 150 )
11X-RAY DIFFRACTION11chain 'B' and (resid 151 through 212 )
12X-RAY DIFFRACTION12chain 'A' and (resid 4 through 20 )
13X-RAY DIFFRACTION13chain 'A' and (resid 21 through 32 )
14X-RAY DIFFRACTION14chain 'A' and (resid 33 through 51 )
15X-RAY DIFFRACTION15chain 'A' and (resid 52 through 61 )
16X-RAY DIFFRACTION16chain 'A' and (resid 62 through 100E)
17X-RAY DIFFRACTION17chain 'A' and (resid 100G through 116 )
18X-RAY DIFFRACTION18chain 'A' and (resid 117 through 218 )

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